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Data Analyst II - Brain Science

Department: Neural Coding

Data Analyst II – Neural Coding

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

The mission of the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling, and theory.

The Axonal Connectomics team at the Allen Institute for Brain Science is seeking a Data Analyst II. We are developing methods for imaging ‘wires’ in the brain (axons) at high resolution with light microscopy, in order to obtain detailed maps of axonal pathways across the whole brain. The approach relies on generating and processing vast amounts of image data. This requires an efficient pipeline for organization and visualization of images, as well as algorithms for automated alignment and segmentation to enable tracing and analysis of axonal pathways.

The primary responsibilities of this position include implementing automation of the image processing pipeline and assisting with deployment of machine learning tools for automated alignment and segmentation. To accomplish this, the individual will work very closely with experts in infrastructure, alignment, machine learning, and neuroscience to deploy tools to address these various issues.

This position requires a strong background in computational techniques for neuroscience, or a related field, and a desire to work in a fast-paced team environment on large scientific projects.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • Develop tools that support axonal imaging with high-throughput light sheet microscopy
  • Install, test, and scale up existing code for image processing
  • Evaluate and learn new software tools, practices, and algorithms
  • Assist with design and production of deep learning tools for automated alignment and segmentation
  • Contribute to information dissemination (presentations, papers, etc) to the scientific community
  • Willingness to cross-train and perform other duties as assigned

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • Bachelor’s degree in Computer Science, Mathematics, Physics, Engineering, Neuroscience, or Biology
  • Minimum of 2 years of equivalent work experience
  • Experience developing well-documented and tested open-source software

Preferred Education and Experience

  • Experience with microscopy systems or image processing
  • Experience with scientific data visualization
  • Experience using machine learning
  • experience working effectively as part of a collaborative team
  • Aptitude for and interest in computer programming
  • 1-2 years experience in Python, or 4 years experience with a variety of programming languages and a demonstrated ability to learn new programming languages

Physical Demands [ADA items only]

  • Fine motor movements in fingers/hands to operate computers and other office equipment

Position Type/Expected Hours of Work

  • Occasional evening and weekend hours required
  • This role is currently working onsite and remotely when possible, due to COVID-19 and our focus on employee safety. We continue to evaluate the safest options for our employees.

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be up to date with vaccinations against COVID-19 as a condition of employment unless a medical or religious accommodation is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance

Additional Comments

  • Please include a cover letter with your application
  • **Please note that this role does not offer relocation assistance**


It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.





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